GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpK in Herbaspirillum seropedicae SmR1

Align Glycerol kinase; EC 2.7.1.30; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK (uncharacterized)
to candidate HSERO_RS02220 HSERO_RS02220 xylulokinase

Query= curated2:Q9X6C9
         (495 letters)



>FitnessBrowser__HerbieS:HSERO_RS02220
          Length = 490

 Score =  139 bits (349), Expect = 3e-37
 Identities = 149/496 (30%), Positives = 223/496 (44%), Gaps = 56/496 (11%)

Query: 5   LALDQGTTSSWAILFTLEGEVVAVAQRAFAQHYPEPGLVEHDPWEIWESQLWAAKEALRR 64
           L +D GT+   A++   +G +VA+A        P P   E  P + W++       A  R
Sbjct: 3   LGIDLGTSEVKAVVIDAQGSLVALAGSTLNVARPHPRWSEQAPADWWQATCDTV--AKLR 60

Query: 65  AGVGPE---AVLALGIANQRE-TTLVWERDTGRPLHPAIVWQDRRTASLCEALRERG--L 118
             +G E   ++ A+G++ Q     L+ ERD    L PAI+W D R+A  C  L  R   L
Sbjct: 61  TQLGSERFGSIRAIGLSGQMHGAVLLDERD--EVLRPAILWSDSRSAPECAELESRAPRL 118

Query: 119 EGLFRARTGLLLDPYFSATKLLWLLERVPGLRERAERGEVCFGTV---DTWLLWNLTGGR 175
            G+     G L  P F+A KLLW+    P L  R         TV     WL   +TG +
Sbjct: 119 HGI----AGNLAMPGFTAPKLLWVARHEPQLFAR-------IATVLLPKDWLRLKMTGRK 167

Query: 176 VHATDPTNASRTLLFHLETLTWDEELLRVLGIPKALLPEVRPSDGDFGETLPGL-----L 230
           V  +DP++A+ TL   +E   W +ELL   G+ +  +P +       G  LP +     L
Sbjct: 168 V--SDPSDAAGTLWLDVEGRNWSDELLAASGMRRDQMPALVDGSAVSGSLLPEVAQAWGL 225

Query: 231 GAPIPIRGVLGDQQAALLGQAALGAGEGKCTYGT-GAFLLLNTGERPVWAEG--GLLTTL 287
            + + + G  GD  A+ +G  A+  G+G  + GT G   ++N   RP           TL
Sbjct: 226 RSDVIVAGGAGDGAASAVGIGAVKPGDGFLSLGTSGVLFVVNDRFRPNPGRAIHAFCHTL 285

Query: 288 A--WHLEGKAAYALEGSVFVAGAA-VGWLREVGLLGESH---EVESLARQVEDAGGVYFV 341
              WH         + SV ++ A+ + W   +  + E     E+E L  Q  +   + F+
Sbjct: 286 PQRWH---------QMSVMLSAASCLRWFCRLCSVDEKSLLAEIEQLDEQACNNAPL-FL 335

Query: 342 PAFTGLGAPHWDPYARGAILGLTRGTTRAHLARAALEGVAFSVGEVAWAMAGAAGLGLKA 401
           P  +G   PH DPYA G   GLT    RA L  A LEGVAF + +   A+  AAG  +  
Sbjct: 336 PYLSGERTPHNDPYATGVFHGLTPEHQRAALGYAVLEGVAFGMVDGLDALR-AAGTDVAE 394

Query: 402 LKADGGMAQNDLFLEIQADLLGVPVLRPRVTET-TALGAAWARGIGAGALSLGDLPALWR 460
           L   GG A++  + ++ AD L V ++    +E   ALGAA    +  G    GD   + R
Sbjct: 395 LSLVGGGARSAYWAQLLADALQVRIVTHVGSEAGGALGAARLAWLADG----GDEAEVCR 450

Query: 461 EEARFLPRMPEARREA 476
           + A+     P+  R A
Sbjct: 451 KPAQQALYQPDPARHA 466


Lambda     K      H
   0.320    0.138    0.434 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 632
Number of extensions: 37
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 495
Length of database: 490
Length adjustment: 34
Effective length of query: 461
Effective length of database: 456
Effective search space:   210216
Effective search space used:   210216
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory